<p>Biogenic iron (Fe)–manganese (Mn) minerals (BFMM) hold strong potential as natural adsorbents for the in-situ immobilization of nitrate (NO₃⁻-N ) in groundwater. Nevertheless, the mechanisms by which Mn-oxidizing bacteria mediate Fe–Mn mineral formation and regulate nitrate behavior remain poorly understood. In this study, a newly isolated Mn‑oxidizing bacterium, <i>Stenotrophomonas</i> sp. Z-MRQA-3, was used to investigate its Mn(II) oxidation capability and the nitrate immobilization performance and mechanisms mediated by the resulting biogenic minerals. Under conditions of 0.5 mM initial Mn(II), 15% NB medium, and a Fe/Mn molar ratio of 2:1, the strain achieved a Mn(II) oxidation efficiency of 45.94%. Structural characterizations (SEM-EDS, BET, and FTIR) revealed that BFMM possesses a high specific surface area (127.74 m²/g), abundant oxygen-containing functional groups (-OH, C = O, and C-O), and irregular particle aggregates with homogeneous Fe and Mn distribution. These structural features underlie its suitability as an adsorbent for nitrate removal. BFMM exhibited a theoretical maximum NO₃⁻-N adsorption capacity of 7.07&#xa0;mg/g, indicating high affinity. The primary immobilization mechanisms involved coordination by surface functional groups in the amorphous mineral matrix and synergistic electrostatic adsorption mediated by multivalent metal ions such as Mn(II/III/IV) and Fe(III). From a microbial-mineral interaction perspective, this work elucidates the key processes through which functional bacteria regulate BFMM formation and couple it with nitrate fixation. These findings advance the understanding of nitrate immobilization mechanisms mediated by biogenic minerals and provide a specific Nature-based Solutions (NbS) technical prototype that is “microbially regulated biomineralization for in-situ nitrate sequestration” to mitigate groundwater nitrate pollution.</p> Graphical Abstract <p></p>